REDItools3 3.2a0__tar.gz → 3.3__tar.gz

{reditools3-3.2a0 → reditools3-3.3}/PKG-INFO

@@ -1,13 +1,13 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: REDItools3
-Version: 3.2a0
+Version: 3.3
 Author: Ernesto Picardi
 Author-email: Adam Handen <adam.handen@gmail.com>
 Project-URL: homepage, https://github.com/BioinfoUNIBA/REDItools3
 Project-URL: repository, https://github.com/BioinfoUNIBA/REDItools3
 Project-URL: issues, https://github.com/BioinfoUNIBA/REDItools3/issues
 Keywords: bioinformatics,RNA,RNA-editing
-Classifier: Development Status :: 3 - Alpha
+Classifier: Development Status :: 5 - Production/Stable
 Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: GNU General Public License (GPL)

{reditools3-3.2a0 → reditools3-3.3}/REDItools3.egg-info/PKG-INFO

@@ -1,13 +1,13 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: REDItools3
-Version: 3.2a0
+Version: 3.3
 Author: Ernesto Picardi
 Author-email: Adam Handen <adam.handen@gmail.com>
 Project-URL: homepage, https://github.com/BioinfoUNIBA/REDItools3
 Project-URL: repository, https://github.com/BioinfoUNIBA/REDItools3
 Project-URL: issues, https://github.com/BioinfoUNIBA/REDItools3/issues
 Keywords: bioinformatics,RNA,RNA-editing
-Classifier: Development Status :: 3 - Alpha
+Classifier: Development Status :: 5 - Production/Stable
 Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: GNU General Public License (GPL)

{reditools3-3.2a0 → reditools3-3.3}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "REDItools3"
-version = "v3.2-alpha"
+version = "v3.3"
 authors = [
   { name="Adam Handen", email="adam.handen@gmail.com" },
   { name="Ernesto Picardi" },
@@ -17,7 +17,7 @@ dependencies = [
 keywords = ["bioinformatics", "RNA", "RNA-editing"]
 requires-python = ">=3.7"
 classifiers = [
-    "Development Status :: 3 - Alpha",
+    "Development Status :: 5 - Production/Stable",
     "Intended Audience :: Developers",
     "Intended Audience :: Science/Research",
     "License :: OSI Approved :: GNU General Public License (GPL)",

{reditools3-3.2a0 → reditools3-3.3}/reditools/analyze.py

@@ -89,7 +89,8 @@ def setup_rtools(options):  # noqa:WPS213,WPS231
         )
 
     if options.bed_file:
-        rtools.load_target_positions(options.bed_file)
+        regions = file_utils.read_bed_file(options.bed_file)
+        rtools.target_positions = regions
     if options.exclude_regions:
         for fname in options.exclude_regions:
             regions = file_utils.read_bed_file(fname)
@@ -208,7 +209,7 @@ def run(options, in_queue, out_queue):
     except Exception as exc:
         if options.debug:
             traceback.print_exception(*sys.exc_info())
-        sys.stderr.write(f'[ERROR] {exc}\n')
+        sys.stderr.write(f'[ERROR] ({type(exc)}) {exc}\n')
 
 
 def parse_options():  # noqa:WPS213

{reditools3-3.2a0 → reditools3-3.3}/reditools/rtchecks.py

@@ -149,12 +149,14 @@ class RTChecks(object):
         Returns:
             (bool): True if there are sufficient edits
         """
-        for num_edits in bases.get_min_edits():
-            if 0 < num_edits < rtools.min_edits_per_nucleotide:
+        for base in "ATCG":
+            if base == bases.ref:
+                continue
+            if bases[base] < rtools.min_edits_per_nucleotide:
                 rtools.log(
                     Logger.debug_level,
                     'DISCARDING COLUMN edits={} < {}',
-                    num_edits,
+                    bases[base],
                     rtools.min_edits_per_nucleotide,
                 )
                 return False